It'd be nice if there was an Engineering mini-game, and that it would look something like the System Shock or Bioshock hacking games. Trip the wrong switch, and something bad happens.

So let's say you're playing a ground STF where you're sneaking around the inside of a Borg cube, but must constantly re-wire their scanners or whatever to evade detection. In a regular STF, the grid would be smaller and have fewer dead ends, but an elite STF would have a much larger grid and have several dead ends. Trip an alarm, and you not only fail the bonus objective, but also get swarmed by drones for the rest of the instance.